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Recent Replies
Answer: Prodigal as ORF finder for eukaryotic genes in metagenome
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Mensur Dlakic
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> Is this use of Prodigal as a heuristic ORF-level detector acceptable when the aim is only to quantify functional, exon part to find domai…
Comment: Diffbind or DESEQ2 Chipseq data
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The [broadPeak file format](https://macs3-project.github.io/MACS/docs/broadPeak.html) is basically a BED file with 9 columns. You can fill …
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> My goal is to obtain coding fragments, exon, for functional profiling, not to reconstruct full eukaryotic gene models
It sounds to me …
Answer: Clustering with other data type than scRNA-seq using Seurat
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As you were told, any dimensionality reduction method could (and probably should) be used here outside of the Seurat package.
In my experi…
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> I am concerned that some known translocations in wheat might not be
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Why would you exclude them? It's genuine biological signal. Just because we/you don't know what these genes are doing doesn't mean that the…
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Sure, Bioc is generic. See for example as a guide here https://bioconductor.org/books/3.21/OSCA.basic/clustering.html#implementation
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I recently updated some of the code and I would like to reintroduce this GitHub open source project:
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Thank you @atpoint and @jaredandrews07 for your help :)
My data is really just a sparse matrix with genes as rows and cells as columns. …
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Yes, extremely high (not always, but sometimes). I think its because of PCR producing non-specific products in low mass conditions (https:/…
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Just a quick comment here: the FinnGen database is mostly built from finnish participants. Due to a founder effect, Finland is quite apart …
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I would skip Seurat entirely here (and generally), and rather use more transparent methods, such as the ones in the Bioconductor framework.…
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Thank you for this clarification. Your clear explanations and generous help are greatly appreciated by everyone here.
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It would be helpful to understand what question you're trying to answer. "Association between two diseases" could mean any or none of the f…
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